Can't really choose to ignore anything in the intro when the game doesn't want to. Also, that's just a ridiculous thing to do in the first place. The intro and the backstory in the vault is so hardcoded that is pretty much impossible to mod something to change it. The rest of the game makes sure that the crap that happened in the intro actually happened. At best you have a mod to completely skip the intro but like i said, the rest of the game still acknowledges that it happened.